Aug 12, 2016

Critically evaluating the theory and performance of Bayesian analysis of macroevolutionary mixtures

Proceedings of the National Academy of Sciences of the United States of America
Brian R MooreJohn P Huelsenbeck

Abstract

Bayesian analysis of macroevolutionary mixtures (BAMM) has recently taken the study of lineage diversification by storm. BAMM estimates the diversification-rate parameters (speciation and extinction) for every branch of a study phylogeny and infers the number and location of diversification-rate shifts across branches of a tree. Our evaluation of BAMM reveals two major theoretical errors: (i) the likelihood function (which estimates the model parameters from the data) is incorrect, and (ii) the compound Poisson process prior model (which describes the prior distribution of diversification-rate shifts across branches) is incoherent. Using simulation, we demonstrate that these theoretical issues cause statistical pathologies; posterior estimates of the number of diversification-rate shifts are strongly influenced by the assumed prior, and estimates of diversification-rate parameters are unreliable. Moreover, the inability to correctly compute the likelihood or to correctly specify the prior for rate-variable trees precludes the use of Bayesian approaches for testing hypotheses regarding the number and location of diversification-rate shifts using BAMM.

  • References13
  • Citations56

Mentioned in this Paper

Peptide Nucleic Acids
Study
Trees (plant)
Wernicke Aphasia
Likelihood Functions
Biological Coevolution
Extinction, Species
Evaluation
Phylogeny
Biodiversity

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